tbuckley/cabot-search huggingface dataset:
Trends and Risk Factors for Venous Thromboembolism Among Hospitalized Medical Patients
Authors: Elad Neeman, Vincent Liu, Pranita Mishra, Khanh K. Thai, James Xu, Heather A. Clancy, David Schlessinger, Raymond Liu
Journal: JAMA Network Open (2022)

Importance While hospital-associated venous thromboembolism (HA-VTE) is a known complication of hospitalization, contemporary incidence and outcomes data are scarce and methodologically contested. Objective To define and validate an automated electronic health record (EHR)–based algorithm for retrospective detection of HA-VTE and examine contemporary HA-VTE incidence, previously reported risk factors, and outcomes. Design, Setting, and Participants This cohort study was conducted using hospital admissions between January 1, 2013, and June 30, 2021, with follow-up until December 31, 2021. All medical (non–intensive care unit) admissions at an integrated health care delivery system with 21 hospitals in Northern California during the study period were included. Data were analyzed from January to June 2022. Exposures Previously reported risk factors associated with HA-VTE and administration of pharmacological prophylaxis were evaluated as factors associated with HA-VTE. Main Outcomes and Measures Yearly incidence rates and timing of HA-VTE events overall and by subtype (deep vein thrombosis, pulmonary embolism, both, or unknown), as well as readmissions and mortality rates. Results Among 1 112 014 hospitalizations involving 529 492 patients (268 797 [50.8%] women; 75 238 Asian [14.2%], 52 697 Black [10.0%], 79 398 Hispanic [15.0%], and 307 439 non-Hispanic White [58.1%]; median [IQR] age, 67.0 [54.0-79.0] years), there were 13 843 HA-VTE events (1.2% of admissions) occurring in 10 410 patients (2.0%). HA-VTE events increased from 307 of 29 095 hospitalizations (1.1%) in the first quarter of 2013 to 551 of 33 729 hospitalizations (1.6%) in the first quarter of 2021. Among all HA-VTE events, 10 746 events (77.6%) were first noted after discharge. In multivariable analyses, several factors were associated with increased odds of HA-VTE, including active cancer (adjusted odds ratio [aOR], 1.96; 95% CI, 1.85-2.08), prior VTE (aOR, 1.71; 95% CI, 1.63-1.79), and reduced mobility (aOR, 1.63; 95% CI, 1.50-1.77). Factors associated with decreased likelihood of HA-VTE included Asian race (vs non-Hispanic White: aOR, 0.65; 95% CI, 0.61-0.69), current admission for suspected stroke (aOR, 0.73; 95% CI, 0.65-0.81), and Hispanic ethnicity (vs non-Hispanic White: aOR, 0.81; 95% CI, 0.77-0.86). HA-VTE events were associated with increased risk of readmission (hazard ratio [HR], 3.33; 95% CI, 3.25-3.41) and mortality (HR, 1.63; 95% CI, 1.57-1.70). Conclusions and Relevance This study found that HA-VTE events occurred in 1.2% of medical admissions, increased over time, and were associated with increased adverse outcomes. These findings suggest that approaches designed to mitigate occurrence and outcomes associated with HA-VTE may remain needed.
Cell identity changes in ocular surface Epithelia
Authors: Nick Di Girolamo, Mijeong Park
Journal: Progress in Retinal and Eye Research (2022)

Corneal and conjunctival epithelia arise from a common ancestral ectoderm cell, then diverge into distinct lineages. The former develops into a multilayered stratified squamous epithelium, the latter into an expansive mucous membrane that stretches the eyelid margin to the cornea's outskirts. The limbus, which intersects these epithelia, is purported to harbor corneal stem cells. Intrinsic programs that prevent these neighbouring epithelia from mixing and changing identity have not been elucidated, however microenvironmental cues that emanate following tissue damage and ensuing disease, dictate cell fate choices including those that influence form and function. Plasticity of ocular surface epithelia is gauged by their ability to undergo epithelial-mesenchymal transition, transdifferentiation, dedifferentiation and metaplastic transformation. Elucidating the molecular mechanism by which these rare and unusual phenomena arise, and persuading cells to either revert to their original state or remain newly committed, could be exploited into game-changing therapeutics for patients with corneal blindness and other diseases.
Multiple nano-drug delivery systems for intervertebral disc degeneration: Current status and future perspectives
Authors: Wenzhao Liu, Zhanjun Ma, Yonggang Wang, Jingjing Yang
Journal: Bioactive Materials (2022)

Low back pain (LBP) is a common disease that imposes a huge social and economic burden on people. Intervertebral disc (IVD) degeneration (IVDD) is often considered to be the leading cause of LBP and further aggravate and cause serious spinal problems. The established treatment strategy for IVDD consists of physiotherapy, pain medication by drug therapy, and, if necessary, surgery, but none of them can be treated from the etiology; that is, it cannot fundamentally reverse IVD and reconstruct the mechanical function of the spine. With the development of nanotechnology and regenerative medicine, nano-drug delivery systems (NDDSs) have improved treatment results because of their good biodegradability, biocompatibility, precise targeted specific drug delivery, prolonged drug release time, and enhanced drug efficacy, and various new NDDSs for drugs, proteins, cells, and genes have brought light and hope for the treatment of IVDD. This review summarizes the research progress of NDDSs in the treatment of IVDD and provides prospects for using NDDSs to address the challenges of IVDD. We hope that the ideas generated in this review will provide insight into the precise treatment of IVDD.
The role of the immune microenvironment in bone, cartilage, and soft tissue regeneration: from mechanism to therapeutic opportunity
Authors: Yuan Xiong, Bo-Bin Mi, Ze Lin, Yi-Qiang Hu, Le Yu, Kang-Kang Zha, Adriana C. Panayi, Tao Yu, Lang Chen, Zhen-Ping Liu, Anish Patel, Qian Feng, Shuan-Hu Zhou, Guo-Hui Liu
Journal: Military Medical Research (2022)

Abstract Bone, cartilage, and soft tissue regeneration is a complex spatiotemporal process recruiting a variety of cell types, whose activity and interplay must be precisely mediated for effective healing post-injury. Although extensive strides have been made in the understanding of the immune microenvironment processes governing bone, cartilage, and soft tissue regeneration, effective clinical translation of these mechanisms remains a challenge. Regulation of the immune microenvironment is increasingly becoming a favorable target for bone, cartilage, and soft tissue regeneration; therefore, an in-depth understanding of the communication between immune cells and functional tissue cells would be valuable. Herein, we review the regulatory role of the immune microenvironment in the promotion and maintenance of stem cell states in the context of bone, cartilage, and soft tissue repair and regeneration. We discuss the roles of various immune cell subsets in bone, cartilage, and soft tissue repair and regeneration processes and introduce novel strategies, for example, biomaterial-targeting of immune cell activity, aimed at regulating healing. Understanding the mechanisms of the crosstalk between the immune microenvironment and regeneration pathways may shed light on new therapeutic opportunities for enhancing bone, cartilage, and soft tissue regeneration through regulation of the immune microenvironment.
Mitochondria and G-quadruplex evolution: an intertwined relationship
Authors: Vinodh J. Sahayasheela, Zutao Yu, Takuya Hidaka, Ganesh N. Pandian, Hiroshi Sugiyama
Journal: Trends in Genetics (2022)

G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes.
CSF proteome profiling across the Alzheimer’s disease spectrum reflects the multifactorial nature of the disease and identifies specific biomarker panels
Authors: Marta del Campo, Carel F. W. Peeters, Erik C. B. Johnson, Lisa Vermunt, Yanaika S. Hok-A-Hin, Mirrelijn van Nee, Alice Chen-Plotkin, David J. Irwin, William T. Hu, James J. Lah, Nicholas T. Seyfried, Eric B. Dammer, Gonzalo Herradon, Lieke H. Meeter, John van Swieten, Daniel Alcolea, Alberto Lleó, Allan I. Levey, Afina W. Lemstra, Yolande A. L. Pijnenburg, Pieter J. Visser, Betty M. Tijms, Wiesje M. van der Flier, Charlotte E. Teunissen
Journal: Nature Aging (2022)
Improving the repeatability of deep learning models with Monte Carlo dropout
Authors: Andreanne Lemay, Katharina Hoebel, Christopher P. Bridge, Brian Befano, Silvia De Sanjosé, Didem Egemen, Ana Cecilia Rodriguez, Mark Schiffman, John Peter Campbell, Jayashree Kalpathy-Cramer
Journal: npj Digital Medicine (2022)

Abstract The integration of artificial intelligence into clinical workflows requires reliable and robust models. Repeatability is a key attribute of model robustness. Ideal repeatable models output predictions without variation during independent tests carried out under similar conditions. However, slight variations, though not ideal, may be unavoidable and acceptable in practice. During model development and evaluation, much attention is given to classification performance while model repeatability is rarely assessed, leading to the development of models that are unusable in clinical practice. In this work, we evaluate the repeatability of four model types (binary classification, multi-class classification, ordinal classification, and regression) on images that were acquired from the same patient during the same visit. We study the each model’s performance on four medical image classification tasks from public and private datasets: knee osteoarthritis, cervical cancer screening, breast density estimation, and retinopathy of prematurity. Repeatability is measured and compared on ResNet and DenseNet architectures. Moreover, we assess the impact of sampling Monte Carlo dropout predictions at test time on classification performance and repeatability. Leveraging Monte Carlo predictions significantly increases repeatability, in particular at the class boundaries, for all tasks on the binary, multi-class, and ordinal models leading to an average reduction of the 95% limits of agreement by 16% points and of the class disagreement rate by 7% points. The classification accuracy improves in most settings along with the repeatability. Our results suggest that beyond about 20 Monte Carlo iterations, there is no further gain in repeatability. In addition to the higher test-retest agreement, Monte Carlo predictions are better calibrated which leads to output probabilities reflecting more accurately the true likelihood of being correctly classified.
Dental sleep-related conditions and the role of oral healthcare providers: A scoping review
Authors: Zhengfei Huang, Ning Zhou, Frank Lobbezoo, Fernanda R. Almeida, Peter A. Cistulli, Marijke Dieltjens, Nelly T. Huynh, Takafumi Kato, Gilles J. Lavigne, Jean-François Masse, Benjamin T. Pliska, Liza van de Rijt, Kate Sutherland, Magdalini Thymi, Olivier M. Vanderveken, Ralph de Vries, Ghizlane Aarab
Journal: Sleep Medicine Reviews (2022)

Dental sleep medicine as a discipline was first described about a quarter of a century ago. Snoring, obstructive sleep apnea, sleep bruxism, xerostomia, hypersalivation, gastroesophageal reflux disease, and orofacial pain were identified as dental sleep-related conditions. This scoping review aimed to: i) identify previously unidentified dental sleep-related conditions; and ii) identify the role of oral healthcare providers in the prevention, assessment, and management of dental sleep-related conditions in adults. A systematic literature search was conducted in PubMed, Embase.com, Web of Science, and Cochrane. Studies that reported an actual or likely role of oral healthcare providers in the prevention, assessment, and/or management of sleep-related conditions were included. Of the 273 included studies, 260 were on previously listed dental sleep-related conditions; the other 13 were on burning mouth syndrome. Burning mouth syndrome was therefore added to the list of dental sleep-related conditions for the first aim and categorized into sleep-related orofacial pain. For the second aim, the role of oral healthcare providers was found to be significant in the prevention, assessment, and management of obstructive sleep apnea and sleep bruxism; in the assessment and management of snoring, sleep-related orofacial pain, and oral dryness; and in the assessment of sleep-related gastroesophageal reflux condition.
An attention residual u-net with differential preprocessing and geometric postprocessing: Learning how to segment vasculature including intracranial aneurysms
Authors: Nan Mu, Zonghan Lyu, Mostafa Rezaeitaleshmahalleh, Jinshan Tang, Jingfeng Jiang
Journal: Medical Image Analysis (2022)

Intracranial aneurysms (IA) are lethal, with high morbidity and mortality rates. Reliable, rapid, and accurate segmentation of IAs and their adjacent vasculature from medical imaging data is important to improve the clinical management of patients with IAs. However, due to the blurred boundaries and complex structure of IAs and overlapping with brain tissue or other cerebral arteries, image segmentation of IAs remains challenging. This study aimed to develop an attention residual U-Net (ARU-Net) architecture with differential preprocessing and geometric postprocessing for automatic segmentation of IAs and their adjacent arteries in conjunction with 3D rotational angiography (3DRA) images.
Identification by cluster analysis of patients with asthma and nasal symptoms using the MASK-air® mHealth app
Authors: J. Bousquet, B. Sousa-Pinto, J.M. Anto, R. Amaral, L. Brussino, G.W. Canonica, A.A. Cruz, B. Gemicioglu, T. Haahtela, M. Kupczyk, V. Kvedariene, D.E. Larenas-Linnemann, R. Louis, N. Pham-Thi, F. Puggioni, F.S. Regateiro, J. Romantowski, J. Sastre, N. Scichilone, L. Taborda-Barata, M.T. Ventura, I. Agache, A. Bedbrook, K.C. Bergmann, S. Bosnic-Anticevich, M. Bonini, L.-P. Boulet, G. Brusselle, R. Buhl, L. Cecchi, D. Charpin, C. Chaves-Loureiro, W. Czarlewski, F. de Blay, P. Devillier, G. Joos, M. Jutel, L. Klimek, P. Kuna, D. Laune, J.L. Pech, M. Makela, M. Morais-Almeida, R. Nadif, M. Niedoszytko, K. Ohta, N.G. Papadopoulos, A. Papi, D.R. Yeverino, N. Roche, A. Sá-Sousa, B. Samolinski, M.H. Shamji, A. Sheikh, C. Suppli Ulrik, O.S. Usmani, A. Valiulis, O. Vandenplas, A. Yorgancioglu, T. Zuberbier, J.A. Fonseca
Journal: Pulmonology (2022)

The self-reporting of asthma frequently leads to patient misidentification in epidemiological studies. Strategies combining the triangulation of data sources may help to improve the identification of people with asthma. We aimed to combine information from the self-reporting of asthma, medication use and symptoms to identify asthma patterns in the users of an mHealth app.We studied MASK-air® users who reported their daily asthma symptoms (assessed by a 0-100 visual analogue scale - "VAS Asthma") at least three times (either in three different months or in any period). K-means cluster analysis methods were applied to identify asthma patterns based on: (i) whether the user self-reported asthma; (ii) whether the user reported asthma medication use and (iii) VAS asthma. Clusters were compared by the number of medications used, VAS asthma levels and Control of Asthma and Allergic Rhinitis Test (CARAT) levels.We assessed a total of 8,075 MASK-air® users. The main clustering approach resulted in the identification of seven groups. These groups were interpreted as probable: (i) severe/uncontrolled asthma despite treatment (11.9-16.1% of MASK-air® users); (ii) treated and partly-controlled asthma (6.3-9.7%); (iii) treated and controlled asthma (4.6-5.5%); (iv) untreated uncontrolled asthma (18.2-20.5%); (v) untreated partly-controlled asthma (10.1-10.7%); (vi) untreated controlled asthma (6.7-8.5%) and (vii) no evidence of asthma (33.0-40.2%). This classification was validated in a study of 192 patients enrolled by physicians.We identified seven profiles based on the probability of having asthma and on its level of control. mHealth tools are hypothesis-generating and complement classical epidemiological approaches in identifying patients with asthma.
An ER-targeted “reserve-release” fluorogen for topological quantification of reticulophagy
Authors: Hongbao Fang, Lianting Hu, Qixin Chen, Shanshan Geng, Kangqiang Qiu, Chengjun Wang, Mingang Hao, Zhiqi Tian, Huimin Chen, Lei Liu, Jun-Lin Guan, Yuncong Chen, Lei Dong, Zijian Guo, Weijiang He, Jiajie Diao
Journal: Biomaterials (2022)
Implementation of infection prevention and control for hospitalized neonates: A narrative review
Authors: Emanuela Nyantakyi, Laura Caci, Marta Castro, Chloé Schlaeppi, Aislinn Cook, Bianca Albers, Joel Walder, Tuuli Metsvaht, Julia Bielicki, Angela Dramowski, Marie-Therese Schultes, Lauren Clack
Journal: Clinical Microbiology and Infection (2022)

BackgroundThe most prevalent infections encountered in neonatal care are healthcare-associated infections. The majority of healthcare-associated infections are considered preventable with evidence-based infection prevention and control (IPC) practices. However, substantial knowledge gaps exist in IPC implementation in neonatal care. Furthermore, the knowledge of factors which facilitate or challenge the uptake and sustainment of IPC programmes in neonatal units is limited. The integration of implementation science approaches in IPC programmes in neonatal care aims to address these problems.ObjectivesThe aim of this narrative review was to identify determinants which have been reported to influence the implementation of IPC programmes and best practices in inpatient neonatal care settings.SourcesA literature search was conducted in PubMed, MEDLINE (Medical Literature Analysis and Retrieval System Online) and CINAHL (Cumulative Index to Nursing and Allied Health Literature) in May 2022. Primary study reports published in English, French, German, Spanish, Portuguese, Italian, Danish, Swedish or Norwegian since 2000 were eligible for inclusion. Included studies focused on IPC practices in inpatient neonatal care settings and reported determinants which influenced implementation processes.ContentThe Consolidated Framework for Implementation Research was used to identify and cluster reported determinants to the implementation of IPC practices and programmes in neonatal care. Most studies reported challenges and facilitators at the organizational level as particularly relevant to implementation processes. The commonly reported determinants included staffing levels, work- and caseloads, as well as aspects of organizational culture such as communication and leadership.ImplicationsThe presented knowledge about factors influencing neonatal IPC can support the design, implementation, and evaluation of IPC practices.
Deciphering variable resistance to novel carbapenem-based β-lactamase inhibitor combinations in a multi-clonal outbreak caused by Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae resistant to ceftazidime/avibactam
Authors: Vincenzo Di Pilato, Luigi Principe, Lilia Andriani, Noemi Aiezza, Marco Coppi, Silvia Ricci, Tommaso Giani, Francesco Luzzaro, Gian Maria Rossolini
Journal: Clinical Microbiology and Infection (2022)
Self-assembled nano-photosensitizer for targeted, activatable, and biosafe cancer phototheranostics
Authors: Ke Cheng, Junyang Qi, Jie Zhang, Huangxu Li, Xiaojie Ren, Wenyu Wei, Lingkuan Meng, Jing Li, Qianqian Li, Huatang Zhang, Wenbin Deng, Hongyan Sun, Lin Mei
Journal: Biomaterials (2022)
Leaving child and adolescent mental health services in the MILESTONE cohort: a longitudinal cohort study on young people's mental health indicators, care pathways, and outcomes in Europe
Authors: Suzanne E Gerritsen, Larissa S van Bodegom, Mathilde M Overbeek, Athanasios Maras, Frank C Verhulst, Dieter Wolke, Dimitris Rizopoulos, Giovanni de Girolamo, Tomislav Franić, Jason Madan, Fiona McNicholas, Moli Paul, Diane Purper-Ouakil, Paramala J Santosh, Ulrike M E Schulze, Swaran P Singh, Cathy Street, Sabine Tremmery, Helena Tuomainen, Gwendolyn C Dieleman, Rebecca Appleton, Nikolina Davidović, Sabrina Ferrari, Federico Fiori, Charlotte Gatherer, Gaëlle Hendrickx, Ingrid Holme, Renaud Jardri, Alfred Kolozsvari, Kate Lievesley, Mathilde Mastroianni, Virginie Maurice, Giorgia Morini, Aesa Parenti, Frédérick Russet, Melanie Saam, Ilyas Sagar-Ouriaghli, Anne Sartor, Giulia Signorini, Jatinder Singh, Priya Tah, Amanda Tuffrey, Therese AMJ van Amelsvoort, Pamela Varvara, Stefano Vicari, Leanne Walker, Anna Wilson, Helena Jerkovic
Journal: The Lancet Psychiatry (2022)
Antitumor Activity of Anti‐miR‐21 Delivered through Lipid Nanoparticles
Authors: Zhongkun Zhang, Yirui Huang, Jing Li, Fei Su, Jimmy Chun‐Tien Kuo, Yingwen Hu, Xiaobin Zhao, Robert J. Lee
Journal: Advanced Healthcare Materials (2022)

The ability of lipid nanoparticles (LNPs) to deliver nucleic acids have shown a great therapeutic potential to treat a variety of diseases. Here, an optimized formulation of QTsome lipid nanoparticles (QTPlus) is utilized to deliver an anti-miR-21 (AM21) against cancer. The miR-21 downstream gene regulation and antitumor activity is evaluated using mouse and human cancer cells and macrophages. The antitumor activity of QTPlus encapsulating AM21 (QTPlus-AM21) is further evaluated in combination with erlotinib and atezolizumab (ATZ). QTPlus-AM21 demonstrates a superior miR-21-dependent gene regulation and eventually inhibits A549 non-small cell lung cancer growth in vitro. QTPlus-AM21 further induces chemo-sensitization of A549 cells to erlotinib with a combination index of 0.6 in inhibiting A549 cell growth. When systemically administers to MC38 tumor-bearing mouse model, QTPlus-AM21 exhibits an antitumor immune response with over 80% tumor growth inhibition (TGI%) and over twofold and fourfold PD-1 and PD-L1 upregulation in tumors and spleens. The combination therapy of QTPlus-AM21 and ATZ further shows a higher antitumor response (TGI% over 90%) and successfully increases M1 macrophages and CD8 T cells into TME. This study provides new insights into the antitumor mechanism of AM21 and shows great promise of QTPlus-AM21 in combination with chemotherapies and immunotherapies.